A particular difficulty of transporting perishable items is that such items must be maintained within a temperature range to reduce or prevent, depending on the items, spoilage, or conversely damage from freezing. A transport refrigeration unit is used to maintain proper temperatures within a transport cargo space. The transport refrigeration unit can be under the direction of a controller to generate and/or maintain a selected environment (e.g., thermal environment) within the transport cargo space. A controlled atmosphere system for a transport refrigeration system can control atmospheric composition; for example, within the transport cargo space.